Engineered proteins, and methods of making and using

ABSTRACT

The present invention provides engineered proteins and biomedical products made from the engineered proteins. The biomedical products include lenses useful for ophthalmic purposes.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No. 60/538,844, which was filed Jan. 23, 2004, and U.S. Provisional Application No. 60/552,029, which was filed Mar. 10, 2004, which are both hereby incorporated by reference in their entireties.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

The present invention was developed with funds from the United States Government, NIH grant number R01-HL59987 and NSF grant number BES-9901648. Therefore, the United States Government may have certain fights in the invention.

TECHNICAL FIELD

The present invention pertains to engineered proteins, especially when used to make biomedical moldings such as ophthalmic moldings.

BACKGROUND OF THE INVENTION

The cornea accounts for two-thirds of the refractive power of the human eye. This power can be altered by changing the corneal curvature or by varying the cornea's index of refraction. According to the National Center for Health Statistics, approximately 52% of the United States population wears some form of corrective lenses. While there have been significant advancements over the past decade in refractive surgery to correct myopia, hyperopia, and astigmatism, certain problems remain. Laser in situ keratomileusis (LASIK) and photorefractive keratectomy (PRK) have proven very effective in the correction of myopia, astigmatism, and low-moderate hyperopia. Principle limitations of these procedures are their lack of reversibility and limited efficacy in the correction of hyperopia and high myopia.

Recently, with FDA approval of a phakic intraocular lens (IOL) [Verisyse, Advanced Medical Optics Santa Ana, Calif.], there is a potentially improved means to treat high myopia. While these phakic IOLs provide excellent quality of vision to implanted myopes, they can be associated with severe intraocular complications such as endophthalmitis and corneal decompensation . Additionally, these IOLs are not as safe to implant in patients with hyperopia who tend to have shallow anterior chambers and are at increased risk for corneal damage from the implant.

These problems with current refractive surgical approaches have renewed interest in intracorneal implants (inlays) to treat hyperopia and high myopia. Implanting a lenticule in the cornea to correct refractive error is not a new idea. In 1949, Barraquer described implantation of 6 mm flint glass intracorneal lenses in a rabbit model . The corneas developed stromal necrosis and the lenses were extruded. Subsequent experiments by Barraquer using polymethylmethacrylate (PMMA) lenses had similar results. He concluded that limited metabolic exchanged across the synthetic onlay was incompatible with corneal viability. In 1967, Dohlman tested a hydrogel inlay made of glyceryl methacrylated in rabbits and cats. These water permeable implants enabled metabolic exchange and were better tolerated by the rabbit cornea; however, by 3 months, they were often extruded. In the cats there was excellent clinical biocompatibility and no extrusion. Other attempts at a synthetic inlay using colloidin, polypropylene, sialastic, and polysulfone were not well tolerated by the cornea, leading to loss of transparency.

Based on the initial promising results with hydrogel inlays, these materials have been the most exhaustively studied in animal models and more recently, in clinical trials. A microporous hydrogel formulation (Nutrapore®) has been incorporated in a corneal inlay (PermaVision®, Anamed Inc., Anaheim, Calif.) and implanted to correct hyperopia and high myopia. These inlays are 5.0 mm in diameter with a central thickness ranging from 25–60 □m. Their water content is 78% and the refractive index is similar to the cornea. Michieletto and co-workers reported on 10 hyperopes implanted with the PermaVision® lens using a microkeratome to create a comeal flap and securing the implant without sutures. While one inlay had to be removed due to decentration, no other eye lost best corrected visual acuity and the lenses appeared to be well tolerated for the 6 month follow up. Notably, no eye was operated that had more than 0.5 diopters of pre-operative astigmatism. Guell et al. reported 6 hyperopic eyes implanted with a PermaVision® inlay. While all eyes were 20/40 or better at 12 months without correction, only 1 eye was 20/20 without correction. The authors concluded that predictability of inlay power “must be improved.” Werblin and co-workers reported use of different hydrogel inlay, the Permalens® (Alcon Labs, Fort Worth, Tex.), to correct high myopia. Inlays ranging from −10.00 to −15.00 diopters were implanted in 5 myopic patients. With a follow up of at least 18 months in all cases, corneal clarity was maintained, but as in the hyperopic inlays, power predictability was a significant issue. In fact, the mean post-operative refractive error was −5.7+2.1 diopters. While these pilot studies using hydrogel inlays for correction of hyperopia and high myopia establish general biocompatibility (some studies have shown cases of perilenticular inflammation or fibrosis), they do reveal the need for adjustability to maximize visual outcomes. Because it is impossible to predict the post-operative refractive error in patients after implantation, a means to post-operatively adjust inlay power would be desirable.

A significant limitation of current hydrogel inlays is their inability to address the important need for post-operative adjustability.

U.S. Pat. No. 4,264,155 (issued to Miyata) discloses soft contact lenses made from collagen gels to which water-soluble organic polyhydroxy polymers, e.g., mucopolysaccharides, polyvinyl alcohols and the like are added, followed by chemical cross-linking of the gels. The polyhydroxy polymeric additives are said to “surround” the strands of the collagen molecules to protect them against microbial degradation. No teaching or suggestion is made in U.S. Pat. No. 4,264,155 of possibly acylating collagen to produce ethylenically unsaturated or polymeric substituted collagen which could then be polymerized to form useful biomedical articles having high biological and tissue acceptability.

It is known e.g. from WO 95/13764 to provide corneal prostheses composed of porous polymeric material for correcting the optical properties of an eye or altering the appearance thereof. Corneal inlays are in general implanted into or onto the cornea of a mammal using surgical methods, for example by making an incision in the stromal tissue of the cornea to form a pocket into which the onlay is placed, and then closing the incision by suturing.

An alternative approach to correction of refractive error is placement of a corneal onlay. This has the advantages of being reversible, surgically simpler, and stable. The idea is that placement of the onlay on the Bowman's layer over the corneal stroma changes the corneal curvature thereby altering the refractive power of the cornea.

One method involves removing the corneal epithelial cell layers of the cornea by scraping, placing a synthetic lenticule directly onto and in intimate contact with the corneal tissue and holding it in place for a period of time which is sufficient for the epithelial cells to recover, grow over the implant and thus fix it in a persistent manner. The initial temporary fixation of the onlay on the cornea is accomplished by the use of a biocompatible glue such as a commercially available collagen- or fibrin-based two components glue. However said glues have not yet proven satisfactory mainly because of severe handling problems.

In view of these and other drawbacks, there is a need for improved materials for biomedical moldings, and in particular, corneal onlays.

BRIEF SUMMARY OF THE INVENTION

The present invention provides an engineered protein and methods of making and using the engineered protein. The engineered protein of the present invention may be any non-naturally occurring protein, peptide, or polypeptide that, when cross-linked, may form a lens with favorable ophthalmic properties. In certain embodiments of the invention, the engineered protein comprises at least one fibronectin domain and at least one elastin domain. The protein may be synthesized according to methods known to one with skill in the art, and may be a recombinant protein or a fusion protein. The fibronectin domain, in certain embodiments, may comprise a CS1, CS5, or type III domain, or an RGD domain. In other specific embodiments, the elastin domain comprises one or a combination of the amino acid sequences VPGVG, VPGKG, VPGIG, or a functional equivalent thereof.

In one embodiment, the engineered protein comprises SEQ ID NO:1 (LD-YAVTGRGDSPASSKPIA((VPGIG)₂VPGKG(VPGIG)₂)₄VP)₃. It is also contemplated that the protein may have certain tags, such as a His tag, in order to facilitate purification. One with skill in the art realizes that such tags may be cleaved or otherwise removed, and do not contribute to the material properties of the engineered protein. In one embodiment of the invention, the engineered protein is less than 30 kilodaltons, is less that 15 kildaltons, or is less than 10 kilodaltons.

The protein may be cross-linked according to the present invention. It is contemplated that the cross-linking may be chemical or ultraviolet cross-linking. In certain embodiments, the cross-linking occurs in such a manner as to leave behind a minimum of impurities in the cross-linked product. One with skill in the art realizes that the elastic properties of the engineered protein may be altered by the degree of cross-linking, and that a more rigid product may be formed by increased cross-linking. One with skill in the art also realizes that the increase in cross-linking may be accomplished by altering the design of the protein. For example, in certain embodiments of the invention, the engineered protein is cross-linked via lysine residues in the domain VPGKG. Increasing the number of lysines available for cross-linking may alter the elastic properties of the protein. Thus, the protein in SEQ ID NO:1 may be altered by changing the number of VPGIG repeating blocks versus the number of VPGKG blocks. In certain embodiments, impurities in the cross-linked product can be removed by rinsing or chemical extraction.

In certain embodiments, the invention provides an engineered protein composition comprising strands of repeating blocks of fibronectin-like and elastin-like domains. It is contemplated that the engineered protein composition may also include a repeating block of fibroin, elastin, keratin, collagen or combinations of repeating units.

An embodiment of the present invention is a lens comprising an engineered protein, wherein the engineered protein, wherein the protein is cross-linked. In a specific embodiment, the lens is a contact lens, corneal onlay, corneal inlay or intraocular lens. In another specific embodiment, the product forms corneal graft or corneal patch. The engineered protein products of the present invention are suitable for corneal replacements, wherein all, or a part, of the corneal tissue is replaced with the engineered proteins described herein.

It is contemplated, in certain embodiments, that the lens is biocompatible, optically transparent, resistant to biodegradation, stimulates the adhesion of adjacent cells, and has favorable elastic properties. In one embodiment of the invention, the lens has an elastic modulus of about 0.01 to about 5.0 Mpa. In another embodiment, the lens has an elastic modulus of about 0.05 to about 2.0 Mpa. In another embodiment, the lens is substantially free of endotoxin or other contaminants.

Another embodiment of the invention is a film or coating made from the engineered proteins described herein.

Another embodiment of the invention is a method for correcting the optical properties of an eye by implanting into or onto the cornea a corneal onlay comprising an engineered protein, wherein the protein comprises at least one fibronectin domain and at least one elastin domain.

It is contemplated, in certain embodiments, that an adjustable biomedical implant, for example a comeal implant, can be prepared from the engineered protein by including reactive side chains that are susceptible to photochemical cross-linking. For example, an acryloyl or methacryloyl group may be attached to a lysine side chains of the protein of the present invention. One with skill in the art realizes that the number of amino acid residues in a single engineered protein that have acryloyl or methacryloyl may be adjusted. In certain embodiments of the invention, each engineered protein has at least one modified lysine residue with an acryloyl or methacryloyl group. In other embodiments of the invention, some lysine residues are modified, while others are unmodified. One with skill in the art realizes that changing the number of modified lysine residues yields photocurable variants that have variable material properties. One with skill in the art realizes that other amino acid residues may be similarly modified with reactive side chain that increase the degree of cross-linking. One with skill in the art is aware of techniques in which ophthalmic lenses may be adjusted. See, for example, U.S. Patent Publication Nos. 20030176521 and 20030174375, both of the specifications of which are incorporated by reference herein.

In certain embodiments of the invention, the engineered protein is a low molecular weight protein that provides a basis for changing the local curvature of the implant through patterned irradiation and diffusion of low molecular weight species in response to an osmotic gradient. After the intended shape change is accomplished, the structure is “locked” by further irradiation of the entire implant.

In certain embodiments of invention, the engineered proteins of the present invention are contacted with small molecules that may diffuse through an engineered protein solution and aid the cross-linking or polymerization process.

In certain embodiments of the invention, the engineered proteins of the present invention may form a graft for the replacement for all or part of a cornea.

The foregoing has outlined rather broadly the features and technical advantages of the present invention in order that the detailed description of the invention that follows may be better understood. Additional features and advantages of the invention will be described hereinafter. It should be appreciated that the conception and specific embodiment disclosed may be readily utilized as a basis for modifying or designing other structures for carrying out the same purposes of the present invention. It should also be realized that such equivalent constructions do not depart from the invention as set forth herein. The novel features which are believed to be characteristic of the invention, both as to its organization and method of operation, together with further objects and advantages will be better understood from the following description when considered in connection with the accompanying figures. It is to be expressly understood, however, that each of the figures is provided for the purpose of illustration and description only and is not intended as a definition of the limits of the present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

For a more complete understanding of the present invention, reference is now made to the following descriptions taken in conjunction with the accompanying drawing, in which:

FIG. 1. shows the protein design for the engineered protein material. The full amino acid sequence is shown. The fibronectin-derived domain (to promote interaction with the epithelial cells) and the elastin domain (for structural support flexibility) are shown. There is also a tag for protein identification, for protein purification, and a cleavage site;

FIG. 2 shows an SDS gel and the corresponding Western blot showing the single band that represents the artificial protein which has a molecular weight of 35.1 kDa;

FIG. 3 shows how the engineered protein is cross-linked into onlays. The solution of engineered proteins then underwent a cross-linking reaction after having been molded into corneal onlays. The molds are shown. They are made of PMMA material to create a 6.0 mm onlay;

FIG. 4 shows an image of the onlay;

FIG. 5 shows clinical exam photos depicting the onlay implanted into the cornea immediately after the surgery, 48 hours after surgery, and one week after surgery. The open white arrows show the tucked-in edges of the implanted onlay within the pocket. The black arrows show the trephined wound. Fluorescein dye stains the entire exposed onlay surface. In the photo of the same eye 48 hours later, the reepithelialization process has begun and cells are migrating inward from the periphery, as evidenced by the lack of fluorescein dye in these areas. The black arrows show the edge of the initial wound for comparison. At one week after the surgery, the onlay has been incorporated and completely covered by epithelium. There is no fluorescein staining;

FIG. 6 shows a schematic section of the control eyes; and

FIG. 7 shows a schematic section of the implanted onlays. A low-magnification view with PAS staining shows the onlay in the lamellar pocket. The distorted cornea structure is an artifact of the preservation process.

FIG. 8 shows histologic examination at the 7 day point. (A) At low magnification, Mason trichrome staining shows no staining of the novel onlay material compared to the natural cornea. (B) H & E stained specimens confirm reepithelialization of the onlay surface. (C) Higher magnification reveals the corneal stroma, the onlay, and the overlying epithelium to be 1–2 cell layers thick, typical for regenerating corneal epithelium.

DETAILED DESCRIPTION OF THE INVENTION

I. The Present Invention

The present invention relates to an engineered protein product that can be formed into shaped articles useful in medical applications, including implants for ophthalmology, surgery, orthopedics and cardiology. These materials made from engineered proteins can also be used to replace part of or the entire cornea, i.e. as graft tissue following lamellar or penetrating keratoplasty. The engineered protein materials and products of the present invention may serve as both onlays and inlays. The engineered protein materials and products can be used in cataract surgery to replace the crystalline lens or as a phakic intraocular lens.

In certain embodiments of the invention, the lenses made from engineered proteins have at least one, and in certain embodiments all, of the following favorable ophthalmic properties: biocompatibility; predictable correction of myopia, hyperopia, and astigmatism; ability to correct high order aberrations, particularly spherical aberration, to confer vision better than 20/20; mechanical properties enabling ease of insertion and durability; ability to maintain stable refractive correction over time; ease and low cost manufacture; and, removability.

In preferred embodiments of the invention, the engineered protein product is a corneal onlay. The corneal onlay lenses contemplated by the present invention are constructed from de novo designed proteins, genetically engineered to include domains that provide favorable ophthalmic properties.

In certain embodiments of the invention, the engineered proteins are made from human fibronectin and mammalian elastin. The fibronectin domains, which may contain the amino acid sequence arginine-glycine-aspartic acid (RGD), are designed to facilitate cellular growth and adhesion. The elastin-like domains may make up the bulk of the protein, and are designed to ensure the elasticity of the cross-linked material. The application of engineered proteins as the basis for a corneal onlay has not been considered previously. These proteins have advantages for application in corneal onlays for the following reasons:

-   -   1) RGD sequences are known to promote adhesion to many cell         types.     -   2 ) Elastin-like materials have previously been shown to be         biocompatible.     -   3) Elastin, and elastin-like proteins, are generally resistant         to enzymatic degradation, which extends their expected lifetime         in the cornea.     -   4) Elastin-like proteins exhibit high molecular mobility in         water, which is expected to promote good diffusion of nutrients         through the onlay film.     -   5) The modular design of the protein means that only a few amino         acid domains are present, while the biology of natural proteins         that could be used in corneal onlays, such as collagen, is more         complex.     -   6) The designed protein can be cross-linked using existing         chemistry to produce transparent films, including corneal         lens-shaped films.     -   7) The modulus of the cross-linked protein films is         approximately 0.2 MPa, which is flexible enough for the         application and sufficient to allow good surgical handling.

The corneal onlay as herein described, is capable of being surgically associated with, and preferably attached to, a living cornea so as to change its optical properties (such as correct vision deficiencies of the eye) or to change the appearance of the eye, such as coloration of the pupil. The onlay or a portion thereof may be colored with one or more pigments or dyes as are well known in the field. Colored onlays, and particularly coloration around the pupil area, will result in change of eye coloration on implantation.

The invention also contemplates numerous other uses for the engineered protein polymer compositions. Uses include, but are not limited to the following: manufacture of engineered tissue and organs, including structures such as patches, plugs or tissues of engineered protein material. These and other constructs can be supplemented with cells or used without cellular supplementation. Additional uses include the following: prosthetics, and other implants; tissue scaffolding, induction of differentiation of cells either in vitro or in vivo; repair or dressing of wounds; hemostatic devices; devices or structures for use in tissue repair and support such as sutures, adhesives, surgical and orthopedic screws, and surgical and orthopedic plates; natural coatings or components for synthetic implants; cosmetic implants and supports; repair or structural support for organs or tissues; substance delivery; bioengineering platforms; platforms for testing the effect of substances upon cells; cell culture; and numerous other uses.

II. Definitions

As used herein, the use of the word “a” or “an” when used in conjunction with the term “comprising” in the sentences and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” As used herein “another” may mean at least a second or more. Still further, the terms “having”, “including”, “containing” and “comprising” are interchangeable and one of skill in the art is cognizant that these terms are open ended terms.

As used herein, the term “cDNA” can refer to a single-stranded or double-stranded DNA molecule. For a single-stranded cDNA molecule, the DNA strand is complementary to the messenger RNA (“mRNA”) transcribed from a gene. For a double-stranded stranded cDNA molecule, one DNA strand is complementary to the mRNA and the other is complementary to the first DNA strand.

The term “conservative substitution” is used in reference to proteins or peptides to reflect amino acid substitutions that do not substantially alter the activity (specificity or binding affinity) of the molecule. Typically conservative amino acid substitutions involve substitution one amino acid for another amino acid with similar chemical properties (e.g. charge or hydrophobicity). The following six groups each contain amino acids that are typical conservative substitutions for one another: 1) Alanine (A), Serine (S), Threonine (T); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W). Internalizing peptides of the present invention may be modified to include conservative substitutions, so long as the substitutions do not affect the internalizing ability of the peptide.

As used herein, a “coding sequence” or a “nucleotide sequence encoding” a particular protein is a nucleic acid molecule which is transcribed and translated into a polypeptide in vivo or in vitro when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a start codon at the 5′-terminus and a translation stop codon at the 3′-terminus. A coding sequence can include, but is not limited to, prokaryotic nucleic acid molecules, cDNA from eukaryotic mRNA, genomic DNA from eukaryotic (e.g. mammalian) sources, viral RNA or DNA, and even synthetic nucleotide molecules. A transcription termination sequence will usually be located 3′ to the coding sequence.

As used herein, a protein “domain” refers to a functional unit of a peptide sequence. For example, VPGVG is an elastin domain. Additionally, the CS1 region of fibronectin is a domain. For the purposes of this invention, it is not necessary for a protein domain to have any particular structural or folding properties.

As used herein, the term “engineered protein” refers to a non-naturally-occurring polypeptide. The term encompasses, for example, a polypeptide that comprises one or more changes, including additions, deletions or substitutions, relative to a naturally occurring polypeptide, wherein such changes were introduced by recombinant DNA techniques. The term also encompasses a polypeptide that comprises an amino acid sequence generated by man, an artificial protein, a fusions protein, and a chimeric polypeptide. Those skilled in the art can readily generate engineered proteins useful according to this aspect of the invention. When several desired protein fragments or peptides are encoded in the nucleotide sequence incorporated into a vector, one of skill in the art will appreciate that the protein fragments or peptides may be separated by a spacer molecule such as, for example, a peptide, consisting of one or more amino acids. Generally, the spacer will have no specific biological activity other than to join the desired protein fragments or peptides together, or to preserve some minimum distance or other spatial relationship between them. However, the constituent amino acids of the spacer may be selected to influence some property of the molecule such as the folding, net charge, or hydrophobicity. Nucleotide sequences encoding for the production of residues which may be useful in purification of the expressed recombinant protein may be built into the vector. Such sequences are known in the art. For example, a nucleotide sequence encoding for a poly histidine sequence may be added to a vector to facilitate purification of the expressed recombinant protein on a nickel column. Once expressed, recombinant peptides, polypeptides and proteins can be purified according to standard procedures known to one of ordinary skill in the art, including ammonium sulfate precipitation, affinity columns, column chromatography, gel electrophoresis and the like. Substantially pure compositions of about 50 to 99% homogeneity are preferred, and 80 to 95% or greater homogeneity are most preferred for use as therapeutic agents. Engineered proteins may be produced by any means, including, for example, peptide, polypeptide, or protein synthesis.

As used herein, the term “gene” refers to a DNA molecule that either directly or indirectly encodes a nucleic acid or protein product that has a defined biological activity. One class of genes often encountered in the art is the so-called “reporter gene.” A reporter gene is any gene whose expression is used as a measure of the activity of the control sequences to which it is operably linked. Examples of commonly used reporter genes include, but are not limited to, a beta-galactosidase gene, a chloramphenicol aminotransferase (CAT) gene, a luciferase (luc) gene, and genes encoding fluorescent proteins such as Green Fluorescent Protein (GFP), Blue Fluorescent Protein (BFP), etc. Ideally, reporter genes do not interfere with the underlying biological processes that are the target of the study. However, in some instances, it may be desirable to measure the activity of the control sequences by linking them to a gene whose product does alter the underlying biology of the system in which gene expression is occurring. Such genes, while also reporter genes, are often referred to as “biologically active” genes.

As used herein, the term “genomic DNA” refers to a DNA molecule from which an RNA molecule is transcribed. The RNA molecule is most often a messenger RNA (mRNA) molecule, which is ultimately translated into a protein that has a defined biological activity, but alternatively may be a transfer RNA (tRNA) or a ribosomal RNA (rRNA) molecule, which are mediators of the process of protein synthesis.

As used herein, two nucleic acid molecules are “functionally equivalent” when they share two or more quantifiable biological functions. For example, nucleic acid molecules of different primary sequence may encode identical polypeptides; such molecules, while distinct, are functionally equivalent. In this example, these molecules will also share a high degree of sequence homology. Similarly, nucleic acid molecules of different primary sequence may share activity as a promoter of RNA transcription, wherein said RNA transcription occurs in a specific subpopulation of cells, and responds to a unique group of regulatory substances; such nucleic acid molecules are also functionally equivalent.

As used herein, a “heterologous” region of a DNA construct is an identifiable segment of DNA within or attached to another DNA molecule that is not found in association with the other molecule in nature. An example of a heterologous coding sequence is a construct where the coding sequence itself is not found in nature (e.g. synthetic sequences having codons different from the native gene). Allelic variation or naturally occurring mutational events do not give rise to a heterologous region of DNA as used herein.

As used herein, two nucleic acid molecules are “homologous” when at least about 60% to 75% or preferably at least about 80% or most preferably at least about 90% of the nucleotides comprising the nucleic acid molecule are identical over a defined length of the molecule, as determined using standard sequence analysis software such as Vector NTI, GCG, or BLAST. DNA sequences that are homologous can be identified by hybridization under stringent conditions, as defined for the particular system. Defining appropriate hybridization conditions is within the skill of the art. See e.g. Current Protocols in Molecular Biology, Volume I. Ausubel et al., eds. John Wiley:New York N.Y., pp. 2.10.1–2.10.16, first published in 1989 but with annual updating, wherein maximum hybridization specificity for DNA samples immobilized on nitrocellulose filters may be achieved through the use of repeated washings in a solution comprising 0.1–2×SSC (15–30 mM NaCl, 1.5–3 mM sodium citrate, pH 7.0) and 0.1% SDS (sodium dodecylsulfate) at temperatures of 65–68° C. or greater. For DNA samples immobilized on nylon filters, a stringent hybridization washing solution may be comprised of 40 mM NaPO₄, pH 7.2, 1–2% SDS and 1 mM EDTA. Again, a washing temperature of at least 65–68° C. is recommended, but the optimal temperature required for a truly stringent wash will depend on the length of the nucleic acid probe, its GC content, the concentration of monovalent cations and the percentage of formamide, if any, that was contained in the hybridization solution (Current Protocols in Molecular Biology, Volume I. Ausubel et al., eds. John Wiley:New York N.Y., pp. 2.10.1–2.10.16. 1989 with annual updating).

As used herein, the term “nucleic acid molecule” includes both DNA and RNA and, unless otherwise specified, includes both double-stranded and single-stranded nucleic acids. Also included are molecules comprising both DNA and RNA, either DNA/RNA heteroduplexes, also known as DNA/RNA hybrids, or chimeric molecules containing both DNA and RNA in the same strand. Nucleic acid molecules of the invention may contain modified bases. The present invention provides for nucleic acid molecules in both the “sense” orientation (i.e. in the same orientation as the coding strand of the gene) and in the “antisense” orientation (i.e. in an orientation complementary to the coding strand of the gene).

As used herein, the term “operably linked” refers to an arrangement of nucleic acid molecules wherein the components so described are configured so as to perform their usual function.

The terms “polypeptide”, “peptide”, or “protein” are used herein to designate a linear series of amino acid residues connected one to the other by peptide bonds between the alpha-amino and carboxy groups of adjacent residues. The amino acid residues are preferably in the natural “L” isomeric form. However, residues in the “D” isomeric form can be substituted for any L-amino acid residue, as long as the desired functional property is retained by the polypeptide. In addition, the amino acids, in addition to the 20 “standard” amino acids, include modified and unusual amino acids. Furthermore, it should be noted that a dash at the beginning or end of an amino acid residue sequence indicates either a peptide bond to a further sequence of one or more amino acid residues or a covalent bond to a carboxyl or hydroxyl end group.

As used herein, exogenous DNA may be introduced into a cell by processes referred to as “transduction”, “transfection,” or “transformation.” Transduction refers to the introduction of genetic material, either RNA or DNA, across the membrane of a eukaryotic cell via a vector derived from a virus. Transfection refers to the introduction of genetic material across the membrane of a eukaryotic cell by chemical means such as by calcium phosphate-mediated precipitation, by mechanical means such as electroporation, or by physical means such as bioballistic delivery. Transformation refers to the introduction of genetic material into noneukaryotic cells, such as bacterial cells or yeast cells, by chemical, mechanical, physical or biological means. The genetic material delivered into the cell may or may not be integrated (covalently linked) into chromosomal DNA.

III. The Corneal Epithelium

The cornea serves several important functions for vision, e.g., refracting >80% of the incoming light onto the retina, filtering out harmful UV rays, and maintaining an optical “window.” The cornea is composed of five structural layers: the epithelium, Bowman's layer, stroma, Descemet's membrane, and endothelium. The outermost layer, the corneal epithelium, is a multi-layered structure with a complex arrangement of intercellular junctions, chemical signaling, and nerve endings. Similar to other epithelial layers throughout the body, the corneal epithelium prevents entry of pathogens, provides a barrier against fluid loss, and protects against abrasive wounding. The epithelium is separated from the external environment only by a layer of fluid, the tears.

The corneal epithelium is composed of three types of cells—the basal cells (1 layer), wing cells (1–3 layers), and squamous cells (3–4 layers)—which adhere to one another by tight cell junctions. The basal cells also form strong adhesion complexes with the underlying extracellular matrix and ultimately with Bowman's layer. Bowman's layer, the anterior-most layer of the corneal stroma, is an acellular zone consisting of collagen fibrils and associated proteoglycans which are densely woven in a random fashion into a felt-like matrix. Of the cells in the epithelium, only the basal cells have mitotic capabilities. Like all stratified epithelia in the body, the corneal epithelium is self-renewing; complete cellular turnover occurs every 5–7 days. Generally, after the basal cells undergo mitosis, the daughter cells begin to move outward toward terminal differentiation and eventual desquamation. See C. Hanna et al., “Cell production and migration in the epithelial layer of the cornea,” Arch. Ophthalmol., vol. 64, pp. 536 (1960).

In certain embodiments of the invention, it is contemplated that ophthalmic engineered protein products of the present invention, including corneal onlays, intraocular lenses, or contact lenses, will demonstrate confluent growth of epithelial cells over the surface of the product. Additionally, in some embodiments of the invention, the engineered protein products will demonstrate resistance to degradation and resistance to rejection. In certain embodiments, an engineered protein comprises component that promotes nerve growth through the implant, such a functional fragment of a nerve growth factor. In certain embodiments, where appropriate, a surgical technique may be used to allow the onlays of the present invention to adhere to the corneal stroma by physical adhesion. In other embodiments, the corneal onlay to may adhere to the cornea by means of a bioadhesive glue, such as fibrin tissue glue. In certain embodiments, a surgical pocket or flap between the corneal epithelium and Bowman's layer may be created surgically, or in specific embodiments, through use of a laser. The lenses of the present invention may then be implanted under the flap or in the pocket, without the use of a bioadhesive. One with skill in the art is aware that slight design modifications may be necessary to modify the design of the engineered protein, or the shape of the engineered protein product, to promote certain advantages, such as enhancing adhesion between the onlay and Bowman's Layer in the cornea.

IV. Engineered Proteins

The engineered proteins of the present invention may be any protein that, when cross-linked or formed into a shaped product, has favorable ophthalmic properties, such as elasticity, transparency, biocompatability, etc. In certain embodiments of the invention, the engineered proteins are fusion proteins or chimeric proteins. In certain embodiments of the invention, the engineered proteins are made from a combination of human protein domains from various protein sources. In one embodiment of the invention, the engineered protein comprises at least one domain from a human extracellular matrix protein. In another embodiment of the invention, the human protein domain is a variant of the wild-type protein that has been modified to increase the favorable ophthalmic properties of the engineered protein.

One example of a domain or protein fragment suitable for use in an engineered protein is an elastin domain. Elastin (SEQ ID NO:29) is a structural molecule which offers great strength and flexibility. It is resistant to breakdown. Its sequence largely consists of simple repeating sequences of hydrophobic amino acids. An important feature of elastin which accounts for its unique structure and insolubility is its extensive cross-linking between polypeptide chains that occurs at lysine residues. One typical repeating sequence of elastin is VPGVG. Fibronectin (SEQ ID NO:28) is a modular protein composed of homologous repeats of three prototypical types of domains known as types I, II, and III. Fibronectin type III (FN3) repeats are both the largest and the most common of the fibronectin subdomains. FN3 exhibits functional as well as structural modularity. Sites of interaction with other molecules have been mapped to short stretch of amino acids such as the Arg—Gly—Asp (RGD) sequence found in various FN3 domains. The RGD sequences is involved in interactions with integrin. Small peptides containing the RGD sequence can modulate a variety of cell adhesion invents associated with thrombosis, inflammation, and tumor metastasis. In the cornea, fibronectin is known to play an important role in wound healing: it triggers epithelial cells to grow, migrate and adhere to the underlying extracellular matrix. Some other proteins known to contain an FN3 domain are; Contactin 2 or axonin-1 protein, Collagen alpha 1 chain, Neural cell adhesion protein L1, Leukocyte common antigen., and Contactin protein.

Generally, blocks include groups of repeating amino acids making up a peptide sequence that occurs in a protein. Genetically engineered proteins are qualitatively distinguished from sequential polypeptides found in nature in that the length of their block repeats can be greater (up to several hundred amino acids versus less than ten for sequential polypeptides) and the sequence of their block repeats can be almost infinitely complex. Table 1 depicts examples of genetically engineered blocks. Table 1 and a further description of genetically engineered blocks may be found in Franco A. Ferrari and Joseph Cappello, Biosynthesis of Protein Polymers, in: Protein-Based Materials, (eds., Kevin McGrath and David Kaplan), Chapter 2, pp. 37–60, Birkhauser, Boston (1997). An engineered protein of the present invention may comprise any of the below sequences in any order, in any number of repeats, and in combination with any other suitable domain, such as a fibronectin domain or an elastin domain, to provide a protein that, when formed into a lens or artificial tissue, provides favorable ophthalmic properties. The engineered proteins of the present invention also include functional variants of any of the sequences described herein. In certain embodiments of the invention, a functional variant has at least 80% sequence homology to its reference sequence.

TABLE 1 Protein polymer sequences Polymer Name Monomer Amino Acid Sequence SLP 3 (SEQ ID NO:5) [(GAGAGS)₉GAAGY)] SLP 4 (SEQ ID NO:6) (GAGAGS)_(n) SLP F (SEQ ID NO:7) [(GAGAGS)₉GAAVTGRGDSPASAAGY]_(n) SLP L3.0 (SEQ ID NO:8) [(GAGAGS)₉GAAPGASIKVAVSAGPSAGY]_(n) SLP L3.1 (SEQ ID NO:9) [(GAGAGS)₉GAAPGASIKVAVSGPSAGY]_(n) SLP F9 (SEQ ID NO:10) [(GAGAGS)₉RYVVLPRPVCFEKAAGY]_(n) ELP I (SEQ ID NO:11) [(VPGVG)₄]_(n) SELP 0 (SEQ ID NO:12) [(GVGVP)₈(GAGAGS)₂]_(n) SELP 1 (SEQ ID NO:13) [GAA(VPGVG)₄VAAGY(GAGAGS)₉]_(n) SELP 2 (SEQ ID NO:14) [(GAGAGS)₆GAAGY(GAGAGS)₈(GVGVP)₈]_(n) SELP 3 (SEQ ID NO:15) [(GVGVP)₈(GAGAGS₈]_(n) SELP 4 (SEQ ID NO:16) [(GVGVP)₁₂(GAGAGS)₈]_(n) SELP 5 (SEQ ID NO:17) [(GVGVP)₁₆(GAGAGS)₈]_(n) SELP 6 (SEQ ID NO:18) [(GVGVP)₃₂(GAGAGS)₈]_(n) SELP 7 (SEQ ID NO:19) [(GVGVP)₈(GAGAGS)₆]_(n) SELP 8 (SEQ ID NO:20) [(GVGVP)₈(GAGAGS)₄]_(n) KLP 1.2 (SEQ ID NO:21) [(AKLKLAEAKLELAE)₄]_(n) CLP 1 (SEQ ID NO:22) [GAP(GPP)₄]_(n) CLP 2 (SEQ ID NO:23) {[GAP(GPP)₄]₂GPAGPVGSP}_(n) CLP-CB (SEQ ID NO:24) {[GAP(GPP)₄]₂(GLPGPKGDRGDAGPKGADGSPGPA)GPAGPVGS-P}_(n) CLP 3 (SEQ ID NO:25) (GAPGAPGSQGAPGLQ)_(n)

Repetitive amino acid sequences of selected protein polymers. SLP=silk like protein; SLPF=SLP containing the RGD sequence from fibronectin; SLPL 3/0 and SLPL 3/1=SLP containing two difference sequences from laminin protein; ELP=elastin like protein; SELP=silk elastin like protein; CLP=collagen like protein; CLP-CB=CLP containing a cell binding domain from human collagen; KLP=keratin like protein

Embodiments of the engineered protein include cross-linked protein products. The proteins may be cross-linked by reacting the proteins with a suitable and biocompatible cross-linking agent. Cross-linking agents include, but are not limited to glutaraldehyde, bis(sulfosuccinimidyl) suberate, p-Azidobenzolyl Hydazide, N-5-Azido-2-nitrobenzoyloxysuccinimide, 4-[p-Azidosalicylamido]butylamine-, any other suitable cross-linking agent and any combination thereof. A description and list of various cross-linking agents and a disclosure of methods of performing cross-linking steps with such agents may be found in the Pierce Endogen 2001–2002 Catalog which is hereby incorporated by reference. The engineered protein may be cross-linked by utilizing methods generally known in the art. For example, the engineered protein may be partially or entirely cross-linked by exposing, contacting and/or incubating the engineered protein device with a gaseous cross-linking reagent, liquid cross-linking reagent, light or combination thereof.

An adjustable biomedical implant, for example a corneal implant, can be prepared from the engineered protein by including reactive side chains that are susceptible to photochemical cross-linking. Attachment of acryloyl or methacryloyl groups to the lysine side chains of the protein yields photocurable variants that can be cross-linked by laser irradiation. Inclusion of low molecular weight proteins, similarly functionalized, provides a basis for changing the local curvature of the implant through patterned irradiation and diffusion of low molecular weight species in response to an osmotic gradient. After the intended shape change is accomplished, the structure is “locked” by further irradiation of the entire implant.

Engineered proteins of the present invention may also include therapeutic peptide fragments to provide therapeutic benefit to a patient when the proteins are used, for example, as lenses.

V. Peptide Synthesis

Engineered proteins of the present invention may be synthesized according to peptide synthesis techniques that are well known to those of skill in the art (Bodanszky et al., 1976;) Peptide Synthesis, 1985; Solid Phase Peptide Synthelia, 1984); The Proteins, 1976. Appropriate protective groups for use in such syntheses will be found in the above texts, as well as in Protective Groups in Organic Chemistry, 1973. These synthetic methods involve the sequential addition of one or more amino acid residues or suitable protected amino acid residues to a growing peptide chain. Normally, either the amino or carboxyl group of the first amino acid residue is protected by a suitable, selectively removable protecting group. A different, selectively removable protecting group is utilized for amino acids containing a reactive side group, such as lysine.

Using solid phase synthesis as an example, the protected or derivatized amino acid is attached to an inert solid support through its unprotected carboxyl or amino group. The protecting group of the amino or carboxyl group is then selectively removed and the next amino acid in the sequence having the complementary (amino or carboxyl) group suitably protected is admixed and reacted with the residue already attached to the solid support. The protecting group of the amino or carboxyl group is then removed from this newly added amino acid residue, and the next amino acid (suitably protected) is then added, and so forth. After all the desired amino acids have been linked in the proper sequence, any remaining terminal and side group protecting groups (and solid support) are removed sequentially or concurrently, to provide the final peptide. The peptides of the invention are preferably devoid of benzylated or methylbenzylated amino acids. Such protecting group moieties may be used in the course of synthesis, but they are removed before the peptides are used. Additional reactions may be necessary, as described elsewhere, to form intramolecular linkages to restrain conformation.

VI. Fusion Proteins

The present invention relates to engineered proteins, which may be recombinant proteins. In certain embodiments of the invention, fusion proteins may be useful. Fusion proteins may generally be prepared using standard techniques, including chemical conjugation. Preferably, a fusion protein is expressed as a recombinant protein, allowing the production of increased levels, relative to a non-fused protein, in an expression system. Briefly, DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector. The 3′ end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5′ end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion protein that retains the biological activity of both component polypeptides.

A peptide linker sequence may be employed to separate the first and the second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures. Such a peptide linker sequence is incorporated into the fusion protein using standard techniques well known in the art. Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes. Preferred peptide linker sequences contain Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene 40:39–46, 1985; Murphy et al., Proc. Natl. Acad Sci. USA 83:8258–8262, 1986; U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180. The linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.

The ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5′ to the DNA sequence encoding the first polypeptides. Similarly, stop codons required to end translation and transcription termination signals are only present 3′ to the DNA sequence encoding the second polypeptide.

VII. Protein Expression Systems

The engineered proteins of the present invention may be produced recombinantly. Prokaryote- and/or eukaryote-based systems can be employed for use with the present invention to produce nucleic acid sequences, or their cognate polypeptides, proteins and peptides. Many such systems are commercially and widely available.

The insect cell/baculovirus system can produce a high level of protein expression of a heterologous nucleic acid segment, such as described in U.S. Pat. Nos. 5,871,986, 4,879,236, both herein incorporated by reference, and which can be bought, for example, under the name MAXBAC® 2.0 from INVITROGEN® and BACPACK™ BACULOVIRUS EXPRESSION SYSTEM FROM CLONTECH®.

Other examples of expression systems include STRATAGENE®'s COMPLETE CONTROL™ Inducible Mammalian Expression System, which involves a synthetic ecdysone-inducible receptor, or its pET Expression System, an E. coli expression system. Another example of an inducible expression system is available from INVITROGEN®, which carries the T-REX™ (tetracycline-regulated expression) System, an inducible mammalian expression system that uses the full-length CMV promoter. INVITROGEN® also provides a yeast expression system called the Pichia methanolica Expression System, which is designed for high-level production of recombinant proteins in the methylotrophic yeast Pichia methanolica. One of skill in the art would know how to express a vector, such as an expression construct, to produce a nucleic acid sequence or its cognate polypeptide, protein, or peptide.

It is contemplated that the proteins, polypeptides or peptides produced by the methods of the invention may be “overexpressed”, i.e., expressed in increased levels relative to its natural expression in cells. Such overexpression may be assessed by a variety of methods, including radio-labeling and/or protein purification. However, simple and direct methods are preferred, for example, those involving SDS/PAGE and protein staining or western blotting, followed by quantitative analyses, such as densitometric scanning of the resultant gel or blot. A specific increase in the level of the recombinant protein, polypeptide or peptide in comparison to the level in natural cells is indicative of overexpression, as is a relative abundance of the specific protein, polypeptides or peptides in relation to the other proteins produced by the host cell and, e.g., visible on a gel.

In some embodiments, the expressed proteinaceous sequence forms an inclusion body in the host cell, the host cells are lysed, for example, by disruption in a cell homogenizer, washed and/or centrifuged to separate the dense inclusion bodies and cell membranes from the soluble cell components. This centrifugation can be performed under conditions whereby the dense inclusion bodies are selectively enriched by incorporation of sugars, such as sucrose, into the buffer and centrifugation at a selective speed. Inclusion bodies may be solubilized in solutions containing high concentrations of urea (e.g. 8M) or chaotropic agents such as guanidine hydrochloride in the presence of reducing agents, such as β-mercaptoethanol or DTT (dithiothreitol), and refolded into a more desirable conformation, as would be known to one of ordinary skill in the art

VIII. Proteinaceous Compositions

In certain embodiments, the engineered proteins of the present invention may be a proteinaceous molecule. As used herein, a “proteinaceous molecule,” “proteinaceous composition,” “proteinaceous compound,” “proteinaceous chain” or “proteinaceous material” generally refers, but is not limited to, a protein or polypeptide of at least two amino acids. All the “proteinaceous” terms described above may be used interchangeably herein. Additionally, the terms protein, peptide, and polypeptide may be used interchangeably herein.

In certain embodiments the size of the at least one proteinaceous molecule, or engineered protein, may comprise, but is not limited to, a molecule having about 2 to about 2500 or greater amino molecule residues, and any range derivable therein. The invention includes those lengths of contiguous amino acids of any sequence discussed herein.

As used herein, an “amino molecule” refers to any amino acid, amino acid derivative or amino acid mimic as would be known to one of ordinary skill in the art. In certain embodiments, the residues of the proteinaceous molecule are sequential, without any non-amino molecule interrupting the sequence of amino molecule residues. In other embodiments, the sequence may comprise one or more non-amino molecule moieties. In particular embodiments, the sequence of residues of the proteinaceous molecule may be interrupted by one or more non-amino molecule moieties.

Accordingly, the term “proteinaceous composition” encompasses amino molecule sequences comprising at least one of the 20 common amino acids in naturally synthesized proteins, or at least one modified or unusual amino acid.

In certain embodiments the proteinaceous composition comprises at least one protein, polypeptide or peptide. In further embodiments the proteinaceous composition comprises a biocompatible protein, polypeptide or peptide. As used herein, the term “biocompatible” refers to a substance which produces no significant untoward effects when applied to, or administered to, a given organism according to the methods and amounts described herein. Such untoward or undesirable effects are those such as significant toxicity or adverse immunological reactions. In preferred embodiments, biocompatible protein, polypeptide or peptide containing compositions will generally be mammalian proteins or peptides or synthetic proteins or peptides each essentially free from toxins, pathogens and harmful immunogens.

Proteinaceous compositions may be made by any technique known to those of skill in the art, including the expression of proteins, polypeptides or peptides through standard molecular biological techniques, the isolation of proteinaceous compounds from natural sources, or the chemical synthesis of proteinaceous materials. The nucleotide and protein, polypeptide and peptide sequences for various genes have been previously disclosed, and may be found at computerized databases known to those of ordinary skill in the art. One such database is the National Center for Biotechnology Information's Genbank and GenPept databases. The coding regions for these known genes may be amplified and/or expressed using the techniques disclosed herein or as would be know to those of ordinary skill in the art. Alternatively, various commercial preparations of proteins, polypeptides and peptides are known to those of skill in the art.

In certain embodiments a proteinaceous compound may be purified. Generally, “purified” will refer to a specific or protein, polypeptide, or peptide composition that has been subjected to fractionation to remove various other proteins, polypeptides, or peptides, and which composition substantially retains its activity, as may be assessed, for example, by the protein assays, as would be known to one of ordinary skill in the art for the specific or desired protein, polypeptide or peptide.

It is contemplated that virtually any protein, polypeptide or peptide containing component may be used in the compositions and methods disclosed herein. However, it is preferred that the proteinaceous material is biocompatible. In certain embodiments, it is envisioned that the formation of a more viscous composition will be advantageous in that will allow the composition to be more precisely or easily applied to the tissue and to be maintained in contact with the tissue throughout the procedure. In such cases, the use of a peptide composition, or more preferably, a polypeptide or protein composition, is contemplated. Ranges of viscosity include, but are not limited to, about 40 to about 100 poise. In certain aspects, a viscosity of about 80 to about 100 poise is preferred.

IX. Variants of Proteinaceous Compositions

Amino acid sequence variants of the proteins, polypeptides and peptides of the present invention can be substitutional, insertional or deletion variants. Deletion variants lack one or more residues of the native protein that are not essential for function or immunogenic activity. Another common type of deletion variant is one lacking secretory signal sequences or signal sequences directing a protein to bind to a particular part of a cell. Insertional mutants typically involve the addition of material at a non-terminal point in the polypeptide. This may include the insertion of an immunoreactive epitope or simply a single residue. Terminal additions, called fusion proteins, are discussed below.

Substitutional variants typically contain the exchange of one amino acid for another at one or more sites within the protein, and may be designed to modulate one or more properties of the polypeptide, such as stability against proteolytic cleavage, without the loss of other functions or properties. Substitutions of this kind preferably are conservative, that is, one amino acid is replaced with one of similar shape and charge. Conservative substitutions are well known in the art and include, for example, the changes of: alanine to serine; arginine to lysine; asparagine to glutamine or histidine; aspartate to glutamate; cysteine to serine; glutamine to asparagine; glutamate to aspartate; glycine to proline; histidine to asparagine or glutamine; isoleucine to leucine or valine; leucine to valine or isoleucine; lysine to arginine; methionine to leucine or isoleucine; phenylalanine to tyrosine, leucine or methionine; serine to threonine; threonine to serine; tryptophan to tyrosine; tyrosine to tryptophan or phenylalanine; and valine to isoleucine or leucine.

The term “biologically functional equivalent” is well understood in the art and is further defined in detail herein. Accordingly, sequences that have between about 70% and about 80%; or more preferably, between about 81% and about 90%; or even more preferably, between about 91% and about 99%; of amino acids that are identical or functionally equivalent to the amino acids of the peptide mimetics provided the biological activity of the mimetic is maintained. (see Table 1, below for a list of functionally equivalent codons).

TABLE 2 Codon Table Amino Acids Codons Alanine Ala A GCA GCC GCG GCU Cysteine Cys C UGC UGU Aspartic acid Asp D GAC GAU Glutamic acid Glu E GAA GAG Phenylalanine Phe F UUC UUU Glycine Gly G GGA GGC GGG GGU Histidine His H CAC CAU Isoleucine Ile I AUA AUC AUU Lysine Lys K AAA AAG Leucine Leu L UUA UUG CUA CUC CUG CUU Methionine Met M AUG Asparagine Asn N AAC AAU Proline Pro P CCA CCC CCG CCU Glutamine Gln Q CAA CAG Arginine Arg R AGA AGG CGA CGC CGG CGU Serine Ser S AGC AGU UCA UCC UCG UCU Threonine Thr T ACA ACC ACG ACU Valine Val V GUA GUC GUG GUU Tryptophan Trp W UGG Tyrosine Tyr Y UAC UAU

The following is a discussion based upon changing of the amino acids of a protein to create an equivalent, or even an improved, second-generation molecule. For example, certain amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein's biological functional activity, certain amino acid substitutions can be made in a protein sequence, and in its underlying DNA coding sequence, and nevertheless produce a protein with like properties. It is thus contemplated by the inventors that various changes may be made in the DNA sequences of genes without appreciable loss of their biological utility or activity, as discussed below.

In making such changes, the hydropathic index of amino acids may be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte & Doolittle, 1982). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like.

It also is understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity. U.S. Pat. No. 4,554,101, incorporated herein by reference, states that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with a biological property of the protein. As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine *−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4).

It is understood that an amino acid can be substituted for another having a similar hydrophilicity value and still produce a biologically equivalent and immunologically equivalent protein. In such changes, the substitution of amino acids whose hydrophilicity values are within ±2 is preferred, those that are within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.

As outlined above, amino acid substitutions generally are based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. Exemplary substitutions that take into consideration the various foregoing characteristics are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.

EXAMPLES

The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Example 1 Cloning and Expression of aECM Protein “aE-RGD”

Protein aE-RGD with the amino acid sequence: M-MASMTGGQQMG-HHHHHHH-DDDDK-(LD-YAVTGRGDSPASSKPIA((VPGIG)₂VPGKG(VPGIG)₂)₄VP)₃-LE (SEQ ID NO:1) contains a T7 tag used for identification by western blotting, a 6-His tag that can be used for purification, an enterokinase cleavage site which allows the T7 and 6-His tags to be removed enzymatically, and three alternating repeats of the cell-binding elastin-like domains. The 17-amino acid cell-binding domain, which includes RGD, is taken from the tenth type III domain of fibronectin; it serves as a ligand for the α_(v)β₃ and α₅β₁ integrins. Other cell binding domains, including the CS1 and CS5 domains from fibronectin, have also been genetically engineered into the same design, in place of the RGD domain. The cell-binding domain can be chosen, from these or other potential bioactive domains to elicit the most favorable cellular response. The elastin-like domains are modified versions of the (VPGVG)_(x), motif derived from mammalian elastin. Lysine residues are incorporated into the elastin-like domains to allow specific cross-linking through their nucleophilic side-chains. Other cross-linking chemistries, including photocross-linking, can also be used.

Standard methods for cloning, bacterial growth, protein expression, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and Western blotting were performed to produce aE-RGD. The gene for aE-RGD was placed under control of a T7 bacteriophage promoter in the pET28 expression vector and transformed into the protein expression host, BL21 (DE3)pLysS.

Host cells were grown in a 10 L fermenter (New Brunswick Scientific BioFlo 3000) using “terrific broth” media at pH 7.4. At an optical density of ˜6, protein expression was induced with isopropyl-1-β-D-thiogalactosidase (IPTG); cells were harvested 1.5 hours after induction by centrifugation at 4° C.

Example 2 Purification of aE-RGD Protein

Cells containing the expressed aE-RGD protein were resuspended in TEN buffer (10 mM Tris-HC1, pH 7.5, 1 mM EDTA, 100 mM NaCI) at a concentration of 0.5 g/mL, and frozen at −20° C. The suspension was defrosted, lysing the cells, and shaken with 10 μg/mL of deoxyribonuclease I, 10 μg/mL of ribonuclease A, 5 mM magnesium chloride, and 1 mM phenylmethylsulfonyl fluoride to inhibit proteolysis, at 37″ C for −3 h, or at 4″ C overnight. The lower critical solution temperature (LCST) behavior of aE-RGD, where the protein separates from an aqueous solution as the temperature is raised, allows the protein to be purified by temperature cycling (the LCST of aE-RGD in water is 35° C.). The pH of the cell lysate was adjusted to 9.0, to ensure protein solubility, and centrifuged below the LCST (˜1 h, 39,750 g, 4° C.). To the supernatant (containing the protein), 1 M NaCl was added, and centrifugation was repeated above the LCST (˜1 h, 39,750 g, 37° C.). The pellet was redispersed in water to a concentration of 50–100 mg/mL. The temperature cycling was repeated twice; the purity of the protein (SDS-PAGE) increases each time.

The solution containing the aE-RGD protein was dialyzed at 4° C. for 3 days, to remove contaminants, and lyophilized. The purity and molecular weights of the proteins were verified by SDS-PAGE gels, Western blots, amino acid analysis, and matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS). Endotoxin levels can be reduced to accepted standards through similar purification protocols. Typical 10 L fermentations using these procedures have yielded 1 to 2 grams aE-RGD.

Example 3 Cross-linking aE-RGD to Form Corneal Onlays

Cross-linking aE-RGD with bis(sulfosuccinimidyl) suberate (BS3) in water at 4° C. results in films with elastic modulus 0.2 MPa, which remain transparent at physiological temperatures. Corneal onlay lenses are made with this chemistry using two-piece PMMA molds of 6 mm optic diameter and 7.5 mm radius. All operations are done at 4° C., well below the LCST of aE-RGD, to ensure transparency. For each batch, 20 mg of aE-RGD is dissolved in 55 uL of water, then 2.3 mg of BS3 just dissolved in 20 uL of water is mixed in (the N-hydroxysuccinimidyl ester groups in BS3 are stoichiometric to primary-amines in the protein). The samples are quickly spun (10 sec) on a tabletop centrifuge to remove bubbles introduced in mixing and 12 μL of the mixture is pipetted into each of 5 molds, which are assembled under a weight (−300 g) and cross-linked overnight at 4° C. Several lenses have been tested for elastic modulus, and a value of approximately 0.2 MPa is consistently seen. Contaminants and reaction byproducts are removed by exposing the lenses to excess water and ethanol, and the rinsed lenses are stored in a humidified container until use.

Example 4 Surgery

The rabbits used in the study (n=12) were anesthetized using inhaled 3% isoflurane and topical proparacaine. Throughout the surgery, the vital signs of the animals were carefully monitored including the corneal reflex, heart rate, respiration, and oxygen saturation. Initial attempts to adhere the corneal onlay were unsuccessful. The right eye of each animal was irrigated with betadine solution and a wire lid speculum was placed into the eye. An approximately 7 mm diameter area of the central corneal epithelium was removed by scraping. The corneal onlay was placed in the center of the abraded area. Blinking of the rabbit's eyelid dislodged the onlay. Tisseel® (Fibrinogen tissue sealant) was applied to the abraded cornea and the onlay was placed on the Tisseel®. The Tisseel® solidified to form a visible fibrin clot.

In order to securely adhere the onlay to the abraded cornea, a pocket in the cornea was created as described below. The right eye of each animal was irrigated with betadine solution and a wire lid speculum was placed into the eye. A 3.0 mm trephine was used to create a partial thickness keratotomy, approximately 100–200 microns in depth in the central cornea. The 0.12 forceps and the 69 blade were used to remove the stromal lamella within the trephined area from the base of the keratotomy. This left a circular keratectomy of 3.0 mm in diameter. A sharp pocket blade was used to make a 2 mm wide circular intralamellar pocket at the base of the keratotomy extending circumferentially outwards toward the corneal limbus.

Three groups of corneas were prepared. In group 1, (n=1) the wounds were created but no implants were placed. In group 2 (n=8), the same wounds were constructed and then the 5.0 mm diameter corneal onlay implant was carefully placed on the corneal surface. The implant was tucked 360 degrees into the grooved pocket using a blunt cyclodialysis spatula. No sutures were placed in this group. In group 3 (n=3), the same wound was constructed, the implants were placed in the pocket, and then 9–0 Nylon sutures were placed over the implant to keep it into place. After implantation, the eyes were irrigated with BSS solution. The rabbits were given an injection of Carprofen analgesic (5 mg/kg IM) postoperatively.

Example 5 Clinical Evaluation

Daily evaluation was performed for one week after implantation. The animals were closely followed for any signs of discomfort or wound infection. At any sign of discomfort, the animal was given one drop of topical 0.03% flurbiprofen and Carprofen 5 mg/kg IM q24 hours. The animals' weights were monitored. Slit lamp biomicroscopy was performed every 2–4 days following the initial procedure. Fluorescein staining with blue light was used to assess the re-epithelialization process. The speed and extent of re-epithelialization was noted as well as any signs of inflammation.

Example 6 Histology

Rabbits were euthanized using standard guidelines for large animals consisting of intramuscular Ketamine 35–50 mg/kg and Xylazine 5–10 mg/kg. Each animal also received an intracardiac injection of sodium pentobarbital and underwent bilateral thoracotomy. different time points.

The eyes were fixed in glutaraldehyde solution and examined histologically at different time points. The slides were stained with hematoxylin-eosin (H&E), periodic acid-Schiff (PAS), Mason tnchrome for collagen, and staining for mucopolysaccharides. Stained sections were mounted and viewed by light microscopy. The pattern of epithelial growth over the corneal implant was assessed histologically. The degree of inflammation both within the corneal stroma as well as within the implant was evaluated.

Light microscopy showed that epithelial cells had covered the entire implant of the cornea at the time of histologic examination one week after the surgery. The corneal epithelium overlying the implant was remarkably normal consisting of several cell layers. The interface between the corneal stroma and the implant was unremarkable. In a few cases, the corneal stroma and the corneal implant were notable for a moderate amount of inflammatory cells including lymphocytes and neutrophils. In other cases, the corneal stroma posterior to the implant and the corneal endothelium appeared normal and free of inflammation.

Example 7 Electron Microscopy

Several eyes were examined by electron microscopy. The animals were euthanized and the eyes were fixed as described for light microscopy. Several animals were used for electron microscopy to evaluate the implant and epithelial interface.

Example 8 Clinical Observations

The implants also tolerated the procedure well, as they were relatively easy to manipulate and durable during the surgery as long as they were well hydrated. All of the implants remained intact and well positioned within the circular stromal pocket. There was no difference in maintenance of the implant in the proper position whether sutures were placed or not. In the eyes where sutures were placed, the implants showed some surface wrinkling due to the tension that the sutures placed on the implant. Compared to the controls, initial mild to moderate inflammation was observed in all the eyes with the implants as shown by mild hyperemia of the bulbar conjunctiva and mild corneal stromal edema. There was no significant mucoid or purulent discharge noted in any of the animals.

Epithelialization in all cases initiated at the periphery of the exposed surface of the corneal onlays and progressed inward toward the center. The time required for full epithelialization varied somewhat between individual animals. All of the implant animals (groups 2 and 3) were partially re-epithelialized at the 96 hour time point, and all animals were fully re-epithelialized by the 1 week point. The control eyes in comparison were fully re-epithelialized by 96 hours. The animals tolerated the procedure well and there were no surgical complications.

Example 9 Epithelial Behavior

Normally, epithelial cells are anchored to the underlying basement membrane through adhesion complexes including hemidesmosomes and anchoring fibrils. Electron microscopy is used to look at the onlay-epithelial interface to look for formation of these structures in our long term studies. The next step will be to address the issue of adhesion to underlying Bowman's layer. The addition of a fibrinogen domain to the protein can facilitate adhesion in the presence of thrombin.

REFERENCES

All patents and publications mentioned in the specifications are indicative of the levels of those skilled in the art to which the invention pertains. All patents and publications are herein incorporated by reference to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference.

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Although the present invention and its advantages have been described in detail, it should be understood that various changes, substitutions and alterations can be made herein without departing from the invention as defined by the appended claims. Moreover, the scope of the present application is not intended to be limited to the particular embodiments of the process, machine, manufacture, composition of matter, means, methods and steps described in the specification. As one will readily appreciate from the disclosure, processes, machines, manufacture, compositions of matter, means, methods, or steps, presently existing or later to be developed that perform substantially the same function or achieve substantially the same result as the corresponding embodiments described herein may be utilized. Accordingly, the appended claims are intended to include within their scope such processes, machines, manufacture, compositions of matter, means, methods, or steps. 

1. A lens comprising a crosslinked engineered protein, which comprises repeated blocks of an elastin domain, wherein the lens is optically transparent, resistant to biodegradation, biocompatible, and is in a shape suitable for incorporation into the eye.
 2. The lens of claim 1, wherein the engineered protein further comprises at least one fibronectin domain and the lens stimulates the adhesion of adjacent cells.
 3. The lens of claim 2, wherein the fibronectin domain comprises one of SEQ ID NO: 26 or 27 and the elastin domain comprises one of SEQ ID NO: 2–4, 11, 12–19, or
 20. 4. The lens of claim 1, wherein the engineered protein comprises SEQ ID NO:
 1. 5. The lens of claim 1, wherein the degree of cross-linking is nonuniform.
 6. The lens of claim 1, wherein the cross-linking is in a predetermined pattern.
 7. The lens of claim 1, wherein the lens is capable of further cross-linking.
 8. The lens of claim 1, wherein the engineered protein is modified by the attachment of at least one acryloyl or methacryloyl group to the protein.
 9. The lens of claim 1, wherein the engineered protein is a low molecular weight protein of less than about 15 kilodaltons.
 10. The lens of claim 1, wherein said lens is selected from the group consisting of contact lens, corneal onlay, corneal graft, corneal inlay and intraocular lens.
 11. The lens of claim 1, wherein said lens is a corneal onlay.
 12. The lens of claim 1, wherein said lens has an elastic modulus of about 0.05 MPa to about 2.0 MPa.
 13. An engineered protein, wherein the protein comprises a CS1 or type III fibronectin cell binding domain, and an elastin domain, wherein the fibronectin cell binding domain comprises SEQ ID NO:
 26. 14. An engineered protein, wherein the protein comprises a CS1 or type III fibronectin cell binding domain, and an elastin domain, wherein the fibronectin cell binding domain comprises SEQ ID NO:
 27. 15. An engineered protein, wherein the protein comprises a CS1 or type III fibronectin cell binding domain, and an elastin domain, wherein the protein comprises SEQ ID NO:
 1. 16. The engineered protein of any one of claims 13, 14, or 15, wherein the engineered protein is modified by the attachment of at least one acryloyl or methacryloyl group to the protein.
 17. The engineered protein of any one of claims 13, 14, or 15, wherein the engineered protein is less than about 15 kilodaltons in molecular weight.
 18. A method for correcting the optical properties of an eye comprising the step of implanting into or onto the cornea a corneal onlay which is optically transparent, resistant to biodegradation, biocompatible, and is in a shape suitable for incorporation into the eye, the corneal onlay comprising an engineered protein, wherein the engineered protein comprises a fibronectin cell binding domain and a block repeat polymer of an elastin domain.
 19. A method according to claim 18 wherein the surface of the onlay stimulates the adhesion of cells adjacent to the implanted onlay.
 20. A material for use in a mammalian eye, comprising: a crosslinked engineered protein comprising a polymer of block repeats in a shape compatible with incorporation into the eye wherein the material is biocompatible, transparent to visible light, has a refractive index compatible with vision by the eye, and wherein the material forms a hydrogel in water due to a block repeat content of the engineered protein and which has an elastic modulus in the hydrogel state of about 0.01 MPa to about 5.0 MPa, wherein the block repeats are of an elastin domain, a collagen domain, a keratin domain, or combinations thereof, wherein the elastin domain comprises a sequence selected from the group consisting of SEQ ID NOS: 2–4, 11, 12–20, and combinations thereof, the collagen domain comprises a sequence selected from the group consisting of SEQ ID NOS: 22–23, 25, and mixtures thereof, and the keratin domain comprises SEQ ID NO:
 21. 